AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG024576

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG024576 MtrunA17_Chr8g0391671 97.320 485 10 2 1 485 1 482 0.0 958
MsaG024576 MtrunA17_Chr5g0397811 94.175 103 5 1 200 302 5 106 5.49e-64 202
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG024576 AT1G24610.1 65.895 475 155 4 11 482 4 474 0.0 630
MsaG024576 AT1G14030.1 24.558 452 287 18 23 461 29 439 5.78e-14 74.3
MsaG024576 AT4G20130.1 22.603 438 269 15 55 468 83 474 1.22e-11 67.0

Find 114 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGATTCATCATCCATTAATT+TGG 0.191527 4:+101080799 None:intergenic
CAAATATGATGGTGCTCTTT+TGG 0.205619 4:-101082077 MsaT024576.1:CDS
CTCGATTCCTCAAATGGTTT+AGG 0.230593 4:-101083749 MsaT024576.1:CDS
ACACTTTCCCACCAAATTAA+TGG 0.235094 4:-101080810 MsaT024576.1:CDS
CTATAATTACAGACTTCTTT+TGG 0.248268 4:+101080723 None:intergenic
CATCCATAGCAAAGTAATAA+AGG 0.272419 4:+101082172 None:intergenic
TCGATTCCTCAAATGGTTTA+GGG 0.287954 4:-101083748 MsaT024576.1:CDS
TCCTGAACAATTCTAGCATT+TGG 0.291593 4:+101082407 None:intergenic
TTATTGAAGCAGGGTGCTTC+AGG 0.306570 4:-101080776 MsaT024576.1:CDS
CCACCAAACGGATGCTTATC+TGG 0.313373 4:+101082581 None:intergenic
CTCAAATGGTTTAGGGTTAG+TGG 0.331608 4:-101083741 MsaT024576.1:CDS
TCTTCCCCAGGAAAGAAAAT+AGG 0.342405 4:+101083307 None:intergenic
TGAATTGTGGGCAATGAAAC+TGG 0.345575 4:-101083413 MsaT024576.1:CDS
GAGATGAAGCATCTACTTCT+TGG 0.347456 4:+101082558 None:intergenic
GTGGAAGATACCTTGAGATC+TGG 0.349462 4:+101081953 None:intergenic
TCCAAATGCTAGAATTGTTC+AGG 0.369501 4:-101082408 MsaT024576.1:CDS
CAATTAACCTCCCATGTTCC+CGG 0.370584 4:-101083617 MsaT024576.1:intron
GGAGCAGGTGTAGAGAAATT+TGG 0.377711 4:+101082022 None:intergenic
GAAGTAGATGCTTCATCTCT+TGG 0.384991 4:-101082554 MsaT024576.1:CDS
CATGGTAACAAGCAATCAAA+TGG 0.388478 4:-101082491 MsaT024576.1:CDS
CACCCACATCTTTGTGCTAC+CGG 0.389753 4:+101082376 None:intergenic
AGTACTCCTTGCAAGTGATA+TGG 0.393467 4:-101080954 MsaT024576.1:CDS
CTTCATGAAAGGGCAAAACT+TGG 0.399181 4:-101083379 MsaT024576.1:CDS
GCTCAAAATCAAGAAGAAAT+CGG 0.402032 4:+101082636 None:intergenic
TGGAAGATACCTTGAGATCT+GGG 0.409477 4:+101081954 None:intergenic
GCAATTAGGTCAGTACCAAT+TGG 0.411464 4:+101083704 None:intergenic
GCACAACTCGATTCCTCAAA+TGG 0.416692 4:-101083755 MsaT024576.1:CDS
CACTAACCCTAAACCATTTG+AGG 0.419235 4:+101083742 None:intergenic
ATCCACACGATCTCATCAAA+TGG 0.420118 4:-101083820 MsaT024576.1:CDS
GACCCTTTATTACTTTGCTA+TGG 0.431078 4:-101082175 MsaT024576.1:CDS
CTGGTTAATATGGTTATAGT+TGG 0.431597 4:-101083953 None:intergenic
AATAATAGAAGGTCGTTTGT+TGG 0.431982 4:-101080987 MsaT024576.1:CDS
TTAGATGCTGAGGCTCCTCT+TGG 0.432705 4:-101080893 MsaT024576.1:CDS
ATCCATAGCAAAGTAATAAA+GGG 0.432856 4:+101082173 None:intergenic
TGATTACACATGTCAATTAG+AGG 0.440828 4:+101082440 None:intergenic
GATGAAGATGCGCATGTTAG+TGG 0.442848 4:+101083875 None:intergenic
AAGTGTACCTGGTGAAGAAT+AGG 0.446363 4:+101083262 None:intergenic
TTATAGTTGGTGGTGGTAGT+TGG 0.452028 4:-101083940 MsaT024576.1:CDS
TTGAGCTCGATACAGTCATA+AGG 0.453734 4:+101082097 None:intergenic
TAGGAAGAGTGTAAGTTTGT+GGG 0.460771 4:+101083326 None:intergenic
GTTAATATGGTTATAGTTGG+TGG 0.472157 4:-101083950 None:intergenic
GATGCTGCGAGCATGGCAGC+TGG 0.474563 4:-101082055 MsaT024576.1:CDS
TGAGCTCGATACAGTCATAA+GGG 0.476129 4:+101082098 None:intergenic
TGATGAATCTTTATTGAAGC+AGG 0.476763 4:-101080786 MsaT024576.1:CDS
TTCATCATCCATTAATTTGG+TGG 0.478727 4:+101080802 None:intergenic
CGTTCACCGTGCTGTGAAGA+TGG 0.479946 4:-101083777 MsaT024576.1:CDS
TTCATGTAACAGGTGAGCTT+AGG 0.480929 4:-101081019 MsaT024576.1:intron
ATGTAACAGGTGAGCTTAGG+TGG 0.482998 4:-101081016 MsaT024576.1:intron
TGTGTTGAGGAAGAGCAATT+AGG 0.483022 4:+101083690 None:intergenic
ATAGGAAGAGTGTAAGTTTG+TGG 0.491387 4:+101083325 None:intergenic
CAATTAGGTCAGTACCAATT+GGG 0.491707 4:+101083705 None:intergenic
TTTGAAGCTTCTTCATGAAA+GGG 0.494538 4:-101083389 MsaT024576.1:CDS
GTTTGAAGCTTCTTCATGAA+AGG 0.494844 4:-101083390 MsaT024576.1:CDS
CTCTACACCTGCTCCATGGC+AGG 0.495127 4:-101082014 MsaT024576.1:CDS
TGGTTTAGGGTTAGTGGCTA+AGG 0.496899 4:-101083735 MsaT024576.1:CDS
ACACCAGATAAGCATCCGTT+TGG 0.499859 4:-101082584 MsaT024576.1:CDS
GCTAAGGAAGATATCCCAAT+TGG 0.505887 4:-101083719 MsaT024576.1:CDS
TGTGGGAGATTACTGATGTA+TGG 0.507516 4:+101083343 None:intergenic
GCATTTGGCAGATGAATTGT+GGG 0.511625 4:-101083425 MsaT024576.1:intron
CCAGATAAGCATCCGTTTGG+TGG 0.512174 4:-101082581 MsaT024576.1:CDS
TCAAGAGCATTCAAGTTACA+TGG 0.514609 4:-101082509 MsaT024576.1:CDS
GGTAAAGCTTCTTTCATCAA+AGG 0.514902 4:-101080675 MsaT024576.1:CDS
GGTGGGCAAGAAATAATAGA+AGG 0.517366 4:-101080998 MsaT024576.1:CDS
TAGATGCTTCATCTCTTGGA+TGG 0.521095 4:-101082550 MsaT024576.1:CDS
TCATCATCCATTAATTTGGT+GGG 0.525608 4:+101080803 None:intergenic
ATAAGTTCCTGCCATGGAGC+AGG 0.528390 4:+101082007 None:intergenic
GAAGCTTTACCTTCCTTGAG+AGG 0.528724 4:+101080687 None:intergenic
CTATCTCATCTAAATCTAGC+TGG 0.528818 4:-101081983 MsaT024576.1:CDS
AATGACACACAGAGCAATCA+AGG 0.529045 4:+101080841 None:intergenic
AATATGGTTATAGTTGGTGG+TGG 0.531556 4:-101083947 MsaT024576.1:CDS
TCAATTAGAGGGAGCATCAT+GGG 0.532994 4:+101082452 None:intergenic
TCCACACGATCTCATCAAAT+GGG 0.536822 4:-101083819 MsaT024576.1:CDS
TGGTGGTGGTAGTTGGAAAA+CGG 0.543989 4:-101083933 MsaT024576.1:CDS
GTCAATTAGAGGGAGCATCA+TGG 0.544285 4:+101082451 None:intergenic
ATGGTAACAAGCAATCAAAT+GGG 0.547291 4:-101082490 MsaT024576.1:CDS
TCACAAATCCATAATCAAGA+AGG 0.549483 4:+101082131 None:intergenic
TCTACTTCTTGGCCACCAAA+CGG 0.549674 4:+101082569 None:intergenic
ATCAAATGGGTAACAAGAGA+AGG 0.550397 4:-101083806 MsaT024576.1:CDS
TGTGGCTGAGAAAGCAATCA+AGG 0.555448 4:-101082203 MsaT024576.1:CDS
AGCATTTGGCAGATGAATTG+TGG 0.556575 4:-101083426 MsaT024576.1:intron
CTATGCTCCTATTCTTCACC+AGG 0.562752 4:-101083269 MsaT024576.1:intron
TGGAGAAACCCCAGATCTCA+AGG 0.564415 4:-101081963 MsaT024576.1:intron
AAGCCGGTAGCACAAAGATG+TGG 0.568257 4:-101082379 MsaT024576.1:CDS
GCTTCTTTCATCAAAGGAGA+CGG 0.577964 4:-101080669 MsaT024576.1:CDS
AAGGAGACGGTCACTACTGA+AGG 0.581558 4:-101080656 MsaT024576.1:CDS
GATGAATCTTTATTGAAGCA+GGG 0.583312 4:-101080785 MsaT024576.1:CDS
CACTTGCCATATCACTTGCA+AGG 0.586602 4:+101080948 None:intergenic
CATGGGAGGTTAATTGAAGG+AGG 0.592569 4:+101083624 None:intergenic
AAATTCTTGATGTCTTCCCC+AGG 0.592666 4:+101083295 None:intergenic
TTGATGAGATCGTGTGGATG+AGG 0.593115 4:+101083824 None:intergenic
AAAGTCAAGCATGCATTAGT+CGG 0.594145 4:-101082611 MsaT024576.1:CDS
GCTCTGTGTGTCATTGCACT+AGG 0.596790 4:-101080833 MsaT024576.1:CDS
GAACATGGGAGGTTAATTGA+AGG 0.597020 4:+101083621 None:intergenic
GATTACACATGTCAATTAGA+GGG 0.597579 4:+101082441 None:intergenic
ACTTAAGTCTTTAGATGCTG+AGG 0.601367 4:-101080903 MsaT024576.1:CDS
AAGTGCAGAGGAATGTGTTG+AGG 0.602415 4:+101083677 None:intergenic
CTAAAGACTTAAGTGTGTTG+AGG 0.608231 4:+101080912 None:intergenic
AAATGGGTAACAAGAGAAGG+TGG 0.609234 4:-101083803 MsaT024576.1:CDS
AGATGCTTCATCTCTTGGAT+GGG 0.610544 4:-101082549 MsaT024576.1:CDS
ATTTCTCTACACCTGCTCCA+TGG 0.612721 4:-101082018 MsaT024576.1:CDS
TAGCACAAAGATGTGGGTGA+AGG 0.614670 4:-101082372 MsaT024576.1:intron
AGCCGGTAGCACAAAGATGT+GGG 0.619848 4:-101082378 MsaT024576.1:CDS
GATAGAATAAGTTCCTGCCA+TGG 0.621183 4:+101082001 None:intergenic
ATTGTTCAGGAACAAGAAGC+CGG 0.621234 4:-101082395 MsaT024576.1:CDS
TGTAACAGGTGAGCTTAGGT+GGG 0.630878 4:-101081015 MsaT024576.1:intron
TCATCATCGTTGAAGTGCAG+AGG 0.633506 4:+101083665 None:intergenic
GGAAGATACCTTGAGATCTG+GGG 0.633639 4:+101081955 None:intergenic
GAATTGTGGGCAATGAAACT+GGG 0.634097 4:-101083412 MsaT024576.1:CDS
TGTATCGAGCTCAAATATGA+TGG 0.639565 4:-101082088 MsaT024576.1:CDS
AGGTCATTTGCAACACCAAG+AGG 0.646673 4:+101080878 None:intergenic
TTACTTACCGGGAACATGGG+AGG 0.654333 4:+101083610 None:intergenic
ACCCATTTGATGAGATCGTG+TGG 0.664082 4:+101083818 None:intergenic
GTTGTGCCATCTTCACAGCA+CGG 0.680905 4:+101083771 None:intergenic
TCAAGGTACGAAATACAGCA+AGG 0.687972 4:+101080858 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr4 gene 101080652 101083966 101080652 ID=MsaG024576
Chr4 mRNA 101080652 101083966 101080652 ID=MsaT024576.1;Parent=MsaG024576
Chr4 exon 101080652 101081029 101080652 ID=MsaT024576.1.exon5;Parent=MsaT024576.1
Chr4 CDS 101080652 101081029 101080652 ID=cds.MsaT024576.1;Parent=MsaT024576.1
Chr4 exon 101081964 101082227 101081964 ID=MsaT024576.1.exon4;Parent=MsaT024576.1
Chr4 CDS 101081964 101082227 101081964 ID=cds.MsaT024576.1;Parent=MsaT024576.1
Chr4 exon 101082373 101082672 101082373 ID=MsaT024576.1.exon3;Parent=MsaT024576.1
Chr4 CDS 101082373 101082672 101082373 ID=cds.MsaT024576.1;Parent=MsaT024576.1
Chr4 exon 101083270 101083436 101083270 ID=MsaT024576.1.exon2;Parent=MsaT024576.1
Chr4 CDS 101083270 101083436 101083270 ID=cds.MsaT024576.1;Parent=MsaT024576.1
Chr4 exon 101083618 101083966 101083618 ID=MsaT024576.1.exon1;Parent=MsaT024576.1
Chr4 CDS 101083618 101083966 101083618 ID=cds.MsaT024576.1;Parent=MsaT024576.1
Gene Sequence

>MsaT024576.1

ATGGTTATAGTTGGTGGTGGTAGTTGGAAAACGGCGATGTTAATGTCATCGTCGTTGAGTCACGTGCGTCCACTAACATGCGCATCTTCATCTTCATCTTCATCTTCATCACGAATAGCTCCTCATCCACACGATCTCATCAAATGGGTAACAAGAGAAGGTGGATTCGTTCACCGTGCTGTGAAGATGGCACAACTCGATTCCTCAAATGGTTTAGGGTTAGTGGCTAAGGAAGATATCCCAATTGGTACTGACCTAATTGCTCTTCCTCAACACATTCCTCTGCACTTCAACGATGATGATCGCAACTCTCACTCTCTCCTCCTTCAATTAACCTCCCATGTTCCCGATGAATTGTGGGCAATGAAACTGGGTTTGAAGCTTCTTCATGAAAGGGCAAAACTTGGATCTTTTTGGTGGCCATACATCAGTAATCTCCCACAAACTTACACTCTTCCTATTTTCTTTCCTGGGGAAGACATCAAGAATTTGCACTATGCTCCTATTCTTCACCAGGTAAACAAAAGATGCCGATTTCTTCTTGATTTTGAGCAAAAAGTCAAGCATGCATTAGTCGGTCTTACACCAGATAAGCATCCGTTTGGTGGCCAAGAAGTAGATGCTTCATCTCTTGGATGGGCGATGTCAGCAGTTTCATCAAGAGCATTCAAGTTACATGGTAACAAGCAATCAAATGGGATAAACTTTGACATTCCCATGATGCTCCCTCTAATTGACATGTGTAATCATAGTTTCAATCCAAATGCTAGAATTGTTCAGGAACAAGAAGCCGGTAGCACAAAGATGTGGGTGAAGGTTGTGGCTGAGAAAGCAATCAAGGAAGATGACCCTTTATTACTTTGCTATGGATGTTTAAGCAATGATCTTTTCCTTCTTGATTATGGATTTGTGATACAGTCAAACCCTTATGACTGTATCGAGCTCAAATATGATGGTGCTCTTTTGGATGCTGCGAGCATGGCAGCTGGAGTTTCTTCACCAAATTTCTCTACACCTGCTCCATGGCAGGAACTTATTCTATCTCATCTAAATCTAGCTGGAGAAACCCCAGATCTCAAGGTGAGCTTAGGTGGGCAAGAAATAATAGAAGGTCGTTTGTTGGCTGCACTAAGAGTACTCCTTGCAAGTGATATGGCAAGTGTACAAAAGCATGACCTCAACACACTTAAGTCTTTAGATGCTGAGGCTCCTCTTGGTGTTGCAAATGACCTTGCTGTATTTCGTACCTTGATTGCTCTGTGTGTCATTGCACTAGGACACTTTCCCACCAAATTAATGGATGATGAATCTTTATTGAAGCAGGGTGCTTCAGGTTCAACAGAATTAGCCATTCAGTTCAGAATCCAAAAGAAGTCTGTAATTATAGATGTAATGAAAAACCTCTCAAGGAAGGTAAAGCTTCTTTCATCAAAGGAGACGGTCACTACTGAAGGCTAA
Protein sequence

>MsaT024576.1

MVIVGGGSWKTAMLMSSSLSHVRPLTCASSSSSSSSSRIAPHPHDLIKWVTREGGFVHRAVKMAQLDSSNGLGLVAKEDIPIGTDLIALPQHIPLHFNDDDRNSHSLLLQLTSHVPDELWAMKLGLKLLHERAKLGSFWWPYISNLPQTYTLPIFFPGEDIKNLHYAPILHQVNKRCRFLLDFEQKVKHALVGLTPDKHPFGGQEVDASSLGWAMSAVSSRAFKLHGNKQSNGINFDIPMMLPLIDMCNHSFNPNARIVQEQEAGSTKMWVKVVAEKAIKEDDPLLLCYGCLSNDLFLLDYGFVIQSNPYDCIELKYDGALLDAASMAAGVSSPNFSTPAPWQELILSHLNLAGETPDLKVSLGGQEIIEGRLLAALRVLLASDMASVQKHDLNTLKSLDAEAPLGVANDLAVFRTLIALCVIALGHFPTKLMDDESLLKQGASGSTELAIQFRIQKKSVIIDVMKNLSRKVKLLSSKETVTTEG*